Locus 2563

Sequence ID	3R_DroMel_CAF1
Location	6,936,659 – 6,936,819
Length	160
Max. P	0.935706

overview

Window 2

Location	6,936,659 – 6,936,757
Length	98
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	84.96
Mean single sequence MFE	-30.98
Consensus MFE	-22.62
Energy contribution	-23.26
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.99
Structure conservation index	0.73
SVM decision value	0.65
SVM RNA-class probability	0.811491
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6936659 98 - 27905053
AGCUCCU-----------CGGUUCUAUUUGCUGCCCCUGCUGCUUUGGCU---------GCUCCCGGAGUCGCAAGUCAGUCACUUGCAGGAUGCUCUCGUCCUGCAGCUACACACCA
.......-----------.(((.......((((.(..(((.(((((((..---------....))))))).))).).))))...((((((((((....))))))))))......))). ( -31.00)
>DroPse_CAF1 121823 115 - 1
UGCUUCUACUCCCACCCCUACUCCUAUUU-CUGCUGCUGUUUCUAUGGCUAUUGCUUUUGCUCCUGGAGUCGCA-GUCAGUCACUUGCAGGAUGCUGUCGUCCUGCAGCUACACAC-A
.((..........................-(((((((...(((((.((.....((....)).)))))))..)))-).))).....(((((((((....))))))))))).......-. ( -29.00)
>DroSec_CAF1 85314 97 - 1
AGCUCCU-----------CGGUUCUAUUUGCUGCCCCUGCUGCUUUGGCU---------GCUCCC-GAGUCGCAAGUCAGUCACUUGCAGGAUGCUCUCGUCCUGCAGCUACACACCA
.......-----------.(((.......((.((....)).))..(((((---------((....-.....((((((.....))))))((((((....)))))))))))))...))). ( -29.70)
>DroSim_CAF1 86597 97 - 1
AGCUCCU-----------CGGUUCUAUUUGCUGCCCCUGCUGCUUUGGCU---------GCUCCC-GAGUCGCAAGUCAGUCACUUGCAGGAUGCUCUCGUCCUGCAGCUACACACCA
.......-----------.(((.......((.((....)).))..(((((---------((....-.....((((((.....))))))((((((....)))))))))))))...))). ( -29.70)
>DroYak_CAF1 87302 97 - 1
AGCUCCU-----------CGGUUGUAUUUGCUGCUCCUGCUGCUUUGGCU---------GCUCCC-GAGUCGCAAGUCAGUCACUUGCAGGAUGCUAUCGUCCUGCAGCUACACACCA
(((....-----------.(..((.((((((.((((..((.((....)).---------))....-)))).))))))))..)...(((((((((....))))))))))))........ ( -35.50)
>consensus
AGCUCCU___________CGGUUCUAUUUGCUGCCCCUGCUGCUUUGGCU_________GCUCCC_GAGUCGCAAGUCAGUCACUUGCAGGAUGCUCUCGUCCUGCAGCUACACACCA
(((..........................((((....(((.((((.(((..........)))....)))).)))...))))....(((((((((....))))))))))))........ (-22.62 = -23.26 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	6,936,729 – 6,936,819
Length	90
Sequences	4
Columns	90
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-26.38
Consensus MFE	-25.11
Energy contribution	-25.68
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.26
Structure conservation index	0.95
SVM decision value	1.25
SVM RNA-class probability	0.935706
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6936729 90 + 27905053
CAGGGGCAGCAAAUAGAACCGAGGAGCUGUAACAACACCUCGCAUCCUUGGCUCUUGCUGUUCGCUGUCAAAAGAGAUUUUUUCAAAUUA
(((((((((((...(((.((((((((((((....)))....)).))))))).))))))))))).)))....................... ( -28.30)
>DroSec_CAF1 85383 90 + 1
CAGGGGCAGCAAAUAGAACCGAGGAGCUGUAGCAACACCUCGCAUCCUUGGCUCUAGCUGUUCGCUGUCAAAAGAGAUUUUUUCAAAUUA
((((((((((...((((.((((((((((((....)))....)).))))))).))))))))))).)))....................... ( -28.00)
>DroSim_CAF1 86666 90 + 1
CAGGGGCAGCAAAUAGAACCGAGGAGCUGUAACAACACCUCGCAUCCUUGGCUGUAGCUGUUCGCUGUCAAAAGAGAUUUUUUCAAAUUA
((((((((((..((((..((((((((((((....)))....)).))))))))))).))))))).)))....................... ( -25.50)
>DroYak_CAF1 87371 90 + 1
CAGGAGCAGCAAAUACAACCGAGGAGCUGUAACAACACCUCGCAUCCUUGGCUCUAGCUGUUCGCUGUCAAAAGAGAUUUUUUCAAAUUA
((((((((((........((((((((((((....)))....)).))))))).....))))))).)))....................... ( -23.72)
>consensus
CAGGGGCAGCAAAUAGAACCGAGGAGCUGUAACAACACCUCGCAUCCUUGGCUCUAGCUGUUCGCUGUCAAAAGAGAUUUUUUCAAAUUA
((((((((((...((((.((((((((((((....)))....)).))))))).))))))))))).)))....................... (-25.11 = -25.68 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:24 2006